In 1940, Hezlet passed the "perisher" exam to become a submarine commanding officer, and took command of the obsolete coastal submarine HMS H44 in December.[2] He was then sent to Malta as a "spare CO". He commanded the submarine HMS Unique, one of the "Fighting" 10th Submarine Flotilla based in Malta from 1941 to 1944. The flotilla helped sink over 1,000,000 tonnes of Axis shipping. Hezlet was awarded the DSC for sinking the 11,000 tonne Italian troopship Esperia.[1] He also commanded HMS Ursula[2] on six patrols, and HMS Upholder on one patrol.

Hezlet returned to the UK in September 1941, with Ian McGeoch as his first lieutenant, to take command of Trident again.[2] In May 1942, he was involved in protecting convoys to North Russia.[1] He sank the German ore carrier Hoedur,[1] and picked up survivors from sunk merchant vessels.[1] He also operated on the surface as escort vessel for the large convoy PQ16, and was mentioned in dispatches again. He became a special training officer on the banks of the River Clyde in September 1942, at the informally named "HMS Varbel", training the crews of midget submarines to attack the German battleship Tirpitz.[1] He invented the "Hezlet Rail", bar and strap that kept men aboard the vessel. He was Mentioned in Despatches after commanding the towing submarine HMS Thrasher.[2]

In retirement, Hezlet wrote many books on naval matters. His first book, The Submarine and Sea Power (1967), foresaw the continuing invulnerability of the seaborne nuclear deterrent. In Aircraft and Sea Power (1970), he took the view that the Atlantic could be defended by land-based aircraft and submarines, with no surface vessels.

Hezlet also wrote a history of the Ulster Special Constabulary, the "B Specials", in 1972.[1] He reviewed the use of electricity and electronics in naval warfare in The Electron and Sea Power (1976). He published a memoir, HMS Trenchant at War: from Chatham to the Banka Strait, in 2001, and his last book, the authoritative History of British and Allied Submarine Operations (2002), listed every patrol taken by an Allied submarine in the Second World War.